Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZEB1

Cell type

Cell type Class
Neural
Cell type
Neural Stem Cells
MeSH Description
Self-renewing cells that generate the main phenotypes of the nervous system in both the embryo and adult. Neural stem cells are precursors to both NEURONS and NEUROGLIA.

Attributes by original data submitter

Sample

Alias
E-MTAB-5541:Zeb1_Cb192
Broker name
ArrayExpress
Description
Protocols: Cells were cultured as previously described (Conti et al. 2005), using laminin as a media supplement (20ug/mL), and plated at a density of 28,000/cm2 Cells were fixed sequentially with di(N-succimidyl) glutarate and 1% formaldehyde in phosphate buffered saline and then lysed, sonicated and immunoprecipitated, as previously described (Castro et al., 2011), with an anti-ZEB1 antibody DNA libraries were prepared from 10ng of immunoprecipitated DNA according to the standard Illumina ChIP-seq protocol.
ENA checklist
ERC000011
INSDC center alias
Instituto Gulbenkian de Ciencia
INSDC center name
Instituto Gulbenkian de Ciencia
INSDC first public
2018-04-24T17:03:46Z
INSDC last update
2017-03-06T12:10:52Z
INSDC status
public
SRA accession
ERS1580348
Sample Name
ERS1580348
Title
Zeb1_Cb192
cell_line
stem cell derived cell line
cell_type
neural stem cell
genotype
wild type genotype
growth condition
media
organism
Homo sapiens

Sequenced DNA Library

library_name
Zeb1_Cb192_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cultured as previously described (Conti et al. 2005), using laminin as a media supplement (20ug/mL), and plated at a density of 28,000/cm2 Cells were fixed sequentially with di(N-succimidyl) glutarate and 1% formaldehyde in phosphate buffered saline and then lysed, sonicated and immunoprecipitated, as previously described (Castro et al., 2011), with an anti-ZEB1 antibody DNA libraries were prepared from 10ng of immunoprecipitated DNA according to the standard Illumina ChIP-seq protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
38409384
Reads aligned (%)
64.6
Duplicates removed (%)
33.6
Number of peaks
1321 (qval < 1E-05)

hg38

Number of total reads
38409384
Reads aligned (%)
67.0
Duplicates removed (%)
31.8
Number of peaks
1425 (qval < 1E-05)

Base call quality data from DBCLS SRA